I would like to be able to fully use biomolecules constructed by Jmol. I need to be able to identify chains and color by chain.
Consider 3ixp which has: - chains: 2 (A, D) - polymers: 4 (there is a gap in the middle of each chain, residues lacking coordinates) The biomolecule 1 has 2 copies of the asymmetric unit, so - chains: 4 (A, A, D, D) - polymers: 8 "color chain" makes everything two colors (A, D). "color polymer" colors each fragment of a chain a different color (8 colors). "color property symop" yields two colors, one for the asymmetric unit and one for the copy of it. Questions: 1. How can I color the biomolecule by chain, that is, to get 4 colors for the biomolecule of 3ixp? Will I need to use a script like this? (It works.) select symop=1 and chain=a color lightblue select symop=1 and chain=d color lightgreen select symop=2 and chain=a color pink select symop=2 and chain=d color yellow 2. How do I get Jmol to report a list of the existing chain IDs to javascript? 3. How do I get Jmol to report the number of symops in a biomolecule to javascript? Is there something easier than parsing the REMARK 350 BIOMT ... records out of the header (using "show pdbheader")? 4. How can I identify (hover, pickcallback) which of the "4 chains" an atom belongs to? As stated in the docs, %[symop] does not work -- should that be implemented? Thanks, -Eric ------------------------------------------------------------------------------ Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
